From 21ce317bce2e1b58803bbb1be439161251478568 Mon Sep 17 00:00:00 2001 From: Greg Burri Date: Tue, 22 Dec 2015 12:30:21 +0100 Subject: [PATCH] * Remove ellipses with a too high standard variation. --- Parasitemia/Parasitemia/Classifier.fs | 90 +++++++++------------ Parasitemia/Parasitemia/Config.fs | 1 + Parasitemia/Parasitemia/MatchingEllipses.fs | 2 +- Parasitemia/Parasitemia/Program.fs | 7 +- 4 files changed, 44 insertions(+), 56 deletions(-) diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index a12e595..c54a3b1 100644 --- a/Parasitemia/Parasitemia/Classifier.fs +++ b/Parasitemia/Parasitemia/Classifier.fs @@ -45,6 +45,22 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img let h = img.Height let h_f = float h + // Return 'true' if the point 'p' is owned by e. + // The lines represents all intersections with other ellipses. + let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) = + e.Contains p.X p.Y && + seq { + let c = PointD(e.Cx, e.Cy) + for d1 in lines do + let d2 = Utils.lineFromTwoPoints c p + if d2.Valid + then + let p' = Utils.pointFromTwoLines d1 d2 + yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse. + else + yield true + } |> Seq.forall id + let ellipses = ellipses |> List.map EllipseFlaggedKd // 1) Associate touching ellipses with each ellipses. @@ -59,33 +75,35 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img | _ -> None ) - let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e)) + let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) + + // 2) Remove ellipses with a high standard deviation (high contrast). + let globalStdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq { + for y in 0 .. h - 1 do + for x in 0 .. w - 1 do + yield img.Data.[y, x, 0] |> float }) - // 2) Remove ellipses with a lower percentage of foreground. (taken from the lower score to the highest). - (*for e, neighbors in List.rev ellipsesWithNeigbors do + for e, neighbors in List.rev ellipsesWithNeigbors do let minX, minY, maxX, maxY = ellipseWindow e - let mutable totalElement = 0 - let mutable fgElement = 0 - for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do - for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do - let yf, xf = float y, float x - if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf) + let stdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq { + for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do + for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do + let p = PointD(float x, float y) + if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) then - totalElement <- totalElement + 1 - if fg.Data.[y, x, 0] > 0uy - then - fgElement <- fgElement + 1 + yield img.Data.[y, x, 0] |> float }) - if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell + if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio then - e.Removed <- true*) + e.Removed <- true // 3) Remove ellipses touching the edges. for e in ellipses do if e.isOutside w_f h_f then e.Removed <- true // 4) Remove ellipses with little area. + let minArea = config.RBCMinArea for e, neighbors in ellipsesWithNeigbors do if not e.Removed then @@ -94,34 +112,16 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img let mutable area = 0 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do - let yf, xf = float y, float x - if e.Contains xf yf && - neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf) - then - area <- area + 1 + let p = PointD(float x, float y) + if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) + then + area <- area + 1 - if area < int config.RBCMinArea + if area < int minArea then e.Removed <- true // 5) Define pixels associated to each ellipse and create the cells. - - // Return 'true' if the point 'p' is owned by e. - // The lines represents all intersections with other ellipses. - let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) = - e.Contains p.X p.Y && - seq { - let c = PointD(e.Cx, e.Cy) - for d1 in lines do - let d2 = Utils.lineFromTwoPoints c p - if d2.Valid - then - let p' = Utils.pointFromTwoLines d1 d2 - yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse. - else - yield true - } |> Seq.forall id - ellipsesWithNeigbors |> List.choose (fun (e, neighbors) -> if e.Removed @@ -135,14 +135,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img let mutable darkStainPixels = 0 let mutable nbElement = 0 - let mutable stain_x = 0.0 - let mutable stain_x2 = 0.0 - let mutable stain_y = 0.0 - let mutable stain_y2 = 0.0 - - let mutable sumCoords_y = 0 - let mutable sumCoords_x = 0 - let elements = new Matrix(maxY - minY + 1, maxX - minX + 1) for y in minY .. maxY do for x in minX .. maxX do @@ -151,8 +143,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img then elements.[y-minY, x-minX] <- 1uy nbElement <- nbElement + 1 - sumCoords_y <- sumCoords_y + y - sumCoords_x <- sumCoords_x + x if infection.Data.[y, x, 0] > 0uy then @@ -161,10 +151,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img if parasites.stain.Data.[y, x, 0] > 0uy then stainPixels <- stainPixels + 1 - stain_x <- stain_x + (float x) - stain_x2 <- stain_x2 + (float x) ** 2.0 - stain_y <- stain_y + (float y) - stain_y2 <- stain_y2 + (float y) ** 2.0 if parasites.darkStain.Data.[y, x, 0] > 0uy then diff --git a/Parasitemia/Parasitemia/Config.fs b/Parasitemia/Parasitemia/Config.fs index a1b06e2..261d87b 100644 --- a/Parasitemia/Parasitemia/Config.fs +++ b/Parasitemia/Parasitemia/Config.fs @@ -30,6 +30,7 @@ type Parameters = { maxDarkStainRatio: float + standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation minimumCellArea: float // Factor of RBC area. } diff --git a/Parasitemia/Parasitemia/MatchingEllipses.fs b/Parasitemia/Parasitemia/MatchingEllipses.fs index 2196122..7a4c51b 100644 --- a/Parasitemia/Parasitemia/MatchingEllipses.fs +++ b/Parasitemia/Parasitemia/MatchingEllipses.fs @@ -12,7 +12,7 @@ open Utils // Do not take in account matching score below this when two ellipses are matched. let matchingScoreThreshold1 = 0.6 -// All ellipsee with a score below this is removed. +// All ellipses with a score below this are removed. let matchingScoreThreshold2 = 2. type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) = diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs index ac495b5..5b8c3e4 100644 --- a/Parasitemia/Parasitemia/Program.fs +++ b/Parasitemia/Parasitemia/Program.fs @@ -61,8 +61,8 @@ let main args = Config( { scale = 1. - minRbcRadius = -0.3 - maxRbcRadius = 0.3 + minRbcRadius = -0.35 + maxRbcRadius = 0.35 preFilterSigma = 1.5 @@ -80,7 +80,8 @@ let main args = maxDarkStainRatio = 0.1 - minimumCellArea = 0.3 }) + standardDeviationMaxRatio = 0.65 + minimumCellArea = 0.5 }) match mode with | CmdLine (input, output) -> -- 2.45.2